Conformations of Polypeptide Chains

To understand how a polypeptide chain folds we need to look carefully at the possible conformations of the peptide units. Since each peptide unit is nearly planar, we can think of a polypeptide as a chain of flat units fastened together. Every peptide
unit is connected to the next by the α-carbon of an amino acid. This carbon provides two single bonds to the chain and rotation can occur about both of them (except in the cyclic amino acid proline). To specify the conformation of an amino acid unit in a polypeptide chain, we must describe the torsion angles about both of these single bonds. These angles are indicated by the symbols (phi) and (psi) and are assigned the value 180° for the fully extended chain. Each angle is taken as zero for the impossible conformation in which the two chain ends are in the eclipsed conformation. By the same token, the torsion angle (omega) around the C–N bond of the amide is 0° for a planar cis peptide linkage and 180° for the usual trans linkage.
Since both φ and ψ can vary for each residue in a protein, there are a large number of possible conformations. However, many are excluded because they bring certain atoms into collision. This fact can be established readily by study of molecular models.

Some idealized shapes that a 34.5 kDa protein molecule of 300 amino acids might assume.

Two peptide units in the completely extended β conformation. The torsion angles φi, ψi, and ωi are defined as 0° when the main chain atoms assume the cis or eclipsed conformation. The angles in the completely extended chain are all 180°. The distance from one α carbon atom (Cα) to the next in a peptide chain is always 0.38 nm, no matter how the chain is folded.

Using a computer, it is possible to study the whole range of possible combinations of φ and ψ. This has been done for the peptide linkage by Ramachandran. The results are often presented as plots of φ vs ψ (Ramachandran plots or conformational maps)
in which possible combinations of the two angles are indicated by blocked out areas. The original Ramachandran plots were made by representing the atoms as hard spheres of appropriate van der Waals radii. This map was calculated for poly-L-alanine but it would be very similar for most amino acids.
The upper area contains the pairs of torsion angles for the extended structures as well as for collagen. The lower area contains allowed conformations for the right-handed
helices. Most of the observed conformations of peptide units in a real protein fall into these regions. Glycyl residues are an exception. Since glycine has no β-carbon atom, the conformations are less restricted. Out of nearly 1900 non-glycine residues in well-determined protein structures, 66 were found in disallowed areas of the Ramachandran diagram. These were often accommodated by local distortions in bond angles. The positions at which such steric strain occurs are often in regions concerned with function.104b One residue, which lies in a disallowed region. It is located adjacent to the coenzyme site. The possible conformations of proline residues are limited. The angle φ is always –60 ± 20°, while ψ for the residue adjacent to the proline N can be either ~150° or ~ –30°. Typical φ, ψ angles for some regular eptide structures are given.

Potential energy distribution in the φ–ψ plane for a pair of peptide units with alanyl residues calculated using potential parameters of Scheraga and Flory. Contours are drawn at intervals of 1 kcal (4.184 kJ) per mol going down from 0 kcal per mol. The zero contour is dashed. From Ramachandran et al. The points marked x are for the four ideal structures: twisted β structure (β), collagen (C), right-handed α helix (αR), and the less favored left-handed α helix (αL).